Question

R package for single-cell RNA-seq data from fastq to matrix

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yueli7 ▴ 20

@yueli7-8401

Last seen 3.5 years ago

China

Hello,

Anyone know any R packages can treat the single cell from fastq, and change it to matrix? That means from the form of single or pair-end reads, and barcode, not matrix? The output should be tabulate reads and ready use for Seurat.

Thanks in advance for great help!

Best,

Yue

single cell • 4.8k views

ADD COMMENT • link updated 4.8 years ago by Aaron Lun ★ 28k • written 4.8 years ago by yueli7 ▴ 20

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Nearly the same question cross-posted

https://www.biostars.org/p/418251/#419441

ADD REPLY • link 4.8 years ago swbarnes2 ★ 1.4k

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Did you not even try to google this?

ADD REPLY • link 4.8 years ago swbarnes2 ★ 1.4k

score 2 · Answer 1 · 2020-02-28

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Aaron Lun ★ 28k

@alun

Last seen 1 hour ago

The city by the bay

See comments in https://osca.bioconductor.org/overview.html#obtaining-a-count-matrix.

P.S. As amusing as it would be to put a LMGTFY link, I'm guessing you doesn't have access to Google, what with the Great Firewall and all. However, the sentiment from swbarnes2 is valid. I am more willing to help people who have shown some effort to help themselves. If you don't want to spend any time on looking things up, why should I spend any time on helping you? Only my employer has that privilege... and they pay a LOT for it.

ADD COMMENT • link 4.8 years ago Aaron Lun ★ 28k

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Hello, Aaron Lun,

Thank you for your response.

Cellranger and alevin are not R package. I already played with scpipe and scruff. Also,DropletsUtils and tximport/tximeta are not from fastq to matrix.

I mean besides, scpipe and scruff, is there available R package? From fastq to matrix?

I can not find any more.

Thank you again!

Best,

Yue

ADD REPLY • link 4.8 years ago yueli7 ▴ 20

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Cellranger and alevin are not R package.

I would have thought that was obvious enough that it need not be said.

I mean besides, scpipe and scruff, is there available R package? From fastq to matrix?

Well. If you're not satisfied, then there's really only one thing left to do:

https://lmgtfy.com/?q=scRNA-seq+FASTQ+to+counts

ADD REPLY • link 4.8 years ago Aaron Lun ★ 28k

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Hello, Aaron Lun,

Thank you!

The first time I heard lmgtfy.

Thank you again!

Best,

Yue

ADD REPLY • link 4.8 years ago yueli7 ▴ 20